There are still problems in IM v6.6.3-8 (Q16, Windows XP) with this format.
Writing with 'BGRA' creates the same files as with 'BGR' (so, the alpha channel is omitted):
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convert logo: -transparent white BGR:test.bgr
convert logo: -transparent white BGRA:test.bgra
And reading with 'BGRA' doesn't work either here.
First an example that works (transparent logo image written as RGBA, again read as RGBA):
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convert logo: -transparent white RGBA:- | identify -verbose -depth 8 -size 640x480 RGBA:-
You will get the normal image and the 'normal' statistics.
When I read that as 'BGRA', the red and blue channels should be swapped - everything else should be the same. But it isn't:
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convert logo: -transparent white RGBA:- | identify -verbose -depth 8 -size 640x480 BGRA:-
...
Format: BGRA (Raw blue, green, red and alpha samples)
...
Histogram:
306240: ( 0, 0, 0,255) #000000 black
480: ( 1, 1,131,254) #010183FE rgba(1,1,131,0.996078)
480: ( 4, 2, 16,254) #040210FE rgba(4,2,16,0.996078)
...
The resulting image is almost completely black (with sometimes a few colored stripes).
The behaviour was the same in version 6.6.3-7 (with modified coder.xml).